I am a beginner using GATK, so bear with me please.
I am trying to do my variant calling with GATK4 new Mutect2 (not MuTect2), using as --germline-resource the af-only-gnomad.hg38.vcf.gz from the GATK's bundle. The command is pretty much the same as seen in the tutorial: https://software.broadinstitute.org/gatk/documentation/article?id=11136, only updated to allow it to be used in a WES.
My problem is that after successfully completing the variant calling, none of the variants have ID information, although when I compared it to a MuTect2 result several did. Basically, all of them have a "." in that field.
I checked the uncompressed gnomad.hg38.vcf.gz manually and the ID info as rsXXXXXX are there.
Any ideas on why the variant calling is not collecting the ID info from the germline resource to populate the ID field? Thank you!